Internal Reference Taxonomies: Amphibian Pilot

Hi! I think is a good idea the use of an Internal Reference Taxonomy.
Concerning amphibian taxonomy in Italy, for example, we recently experience some issues on the use of a single External Source Taxonomy (ASW)...
Indeed, the Societas Herpetologica Italica (the national authority for Amphibians and Reptiles in Italy: http://www-3.unipv.it/webshi/) follows the more stable taxonomy of Amphibiaweb (http://www.amphibiaweb.org/taxonomy/index.html)... and also the taxonomy used by the Italian committee of the IUCN (http://www.iucn.it/index.php) match more the amphibiaweb taxonomy than that of the ASW.
E.g., Bombina pachypus is considered a species on Amphibiaweb (http://www.amphibiaweb.org/cgi/amphib_query?where-genus=Bombina&where-species=pachypus) and on IUCN.it (http://www.iucn.it/scheda.php?id=-291037272), wihle only a subspecies on ASW (as B. variegata pachypus: http://research.amnh.org/vz/herpetology/amphibia/Amphibia/Anura/Bombinatoridae/Bombina/Bombina-variegata).
E.g., The species Lissotriton meridionalis (ASW: http://research.amnh.org/vz/herpetology/amphibia/Amphibia/Caudata/Salamandridae/Pleurodelinae/Lissotriton/Lissotriton-meridionalis) is not commonly utilized in Europe, but is considered a subspecies, Lissotriton vulgaris meridionalis (http://www.amphibiaweb.org/cgi/amphib_query?where-genus=Lissotriton&where-species=vulgaris , http://www.iucn.it/scheda.php?id=-1405096456)

So, in principle, I agree with the idea to give priority to local external references for taxa that are locally endemic (but some problem will arise if two different local external references don't agree...)
Considering my experience in Italy, for the endemic or almost-endemic species, to follow Amphibiaweb or IUCN.it should be better (more conservative and more accepted by the Italian scientist community).

So, having said that, I propose the following changes to the Internal Reference Taxonomy:

Follow ASW and consider Pelophylax bergeri and only a subspecies of Pelophylax lessonae, P. lessonae bergeri
Reasoning: Also the IUCN.it treats Pelophylax bergeri as a synonymous of Pelophylax lessonae
Consider B. variagata pachypus as a full species: B. pachypus
Reasoning: Bombina pachypus as generally accepted as a full species in Italy (As stated above)
Consider Lissotrion meridionalis only a subspecies of Lissotriton vulgaris (L. vulgaris meridionalis)
Reasoning: For Lissotrion vulgaris complex there is no global consensus on taxonomy; in Europe is more accepted the taxonomy of amphibiaweb (As stated above)
Consider Lissotrion graecus only a subspecies of Lissotriton vulgaris (L. vulgaris graecus)
Reasoning: For Lissotrion vulgaris complex there is no global consensus on taxonomy; in Europe is more accepted the taxonomy of amphibiaweb (As stated above)

Best!
D.

Wow, quite the undertaking @loarie! But the need is warranted. I've been discussing this specific topic as it pertains to A. boreas / A.boreas halophilus with a few other iNatter's since SSAR no longer recognizes the subspecies.

Thanks for the general feedback folks. And @danieleseglie thanks for the specific proposals. Lets use your proposed Bombina variegata split as an example for how things would proceed (and an opportunity to lecture folks about the proper way to make taxonomic changes to keep all existing content in sync using the hopelessly complex and confusing iNaturalist taxon change tools).

You're proposing to deviate from Amphibian Species of the World to instead follow IUCN & Amphibiaweb in elevating the Bombina variegata variegata and Bombina variegata pachypus to species status - which can simultaneously be expressed as splitting Bombina variegata (sensu lato) into Bombina variegata (sensu stricto) and Bombina pachypus

Assuming everyone is onboard with this change, I've made 3 draft taxon changes that would accomplish it. In order I'd do the following:
Step 1: Commit Swap 24092 which would inactivate Taxon 480215 while activating and moving content to Taxon 556621
Step 2: Commit Swap 24093 which would inactivate Taxon 479255 while activating and moving content to Taxon 24500
Step 3: Commit Split 24094 which would inactivate Taxon 24496 and distribute content among Taxon 556621 and Taxon 24500 based on their respective atlases.
(This assumes the targets of the taxon changes exist. In this example, I had to create Taxon 556621 but I was able to repurpose Taxon 24500 which was still around from an earlier Taxon Swap I had made in 2015 (looking back, that one should have been a merge rather than a swap, oops).

Yes, I know this is complicated, but these 3 taxon changes are necessary to have all the existing iNat content move to its proper location and keep everything in sync.

Once these taxon changes are made, I (acting as 'amphibian taxonomy czar') would then remove Bombina variegata (sensu lato) [Taxon 24496] from the Internal Reference Taxonomy and add Bombina variegata (sensu stricto) [Taxon 556621] and Bombina pachypus [Taxon 24500].

Does this make sense to everyone? Any objections to implementing this Bombina variegata split? If not, then I'll commit the taxon changes and update the Internal Reference Taxonomy

Perfect! It's all clear to me. I agree with the changes.
Thanks a lot!

@loarie thanks, great! I owe you a beer next time you'll come to Italy (there's a craft brewery near where Daniele lives, and their logo is a toad!) or maybe some wine :-)

Saying "hi" to follow this discussion ;-)

What about adding a few columns to the Google doc where a bunch of things could be documented, eg source taxonomy, reference(s), taxon from which it was split?

@jakob, good idea, I added columns for source and notes to the internal reference taxonomy.

@charlie, the amphibian internal reference taxonomy has columns for family and order which in the case of amphibians are all the nodes in between the root (in this case Class Amphibians) and species. I'd assume if this approach were extended to other taxa that intermediate nodes (family, subgenus etc.) could also be explicitly laid out in the internal reference taxonomy as I've done here with amphibians.

Lastly, looks like ASW has added Pristimantis latro, a newly described Brazilian endemic. Any objections to adding it to our Internal Reference Taxonomy?

I am not an expert, but rather depend on a friend of mine who is the expert for Louisiana herps, Brad Glorioso. He suggested to me that all Dwarf salamnder in Louisiana with the exception of a couple of parishes are now E. paludicola. His words: Actually paludicola is east of the MS River as well. Only extreme Eastern FL Parishes have quadridigitata.

here is the observation that freshened my memory on it and prompted me to check with Brad: https://www.inaturalist.org/observations/8793224

here is his page he keeps up-to-date : http://www.louisianaherps.com/dwarf-salamander-eurycea-qu.html

anyone disagree? should it (or can it) be updated on inat?

http://www.academia.edu/31778175/Revision_of_the_Eurycea_quadridigitata_Holbrook_1842_Complex_of_Dwarf_Salamanders_Caudata_Plethodontidae_Hemidactyliinae_with_a_Description_of_Two_New_Species

Hello @loarie

I wish I had seen this post earlier. I read from the top and there is something that bothers me a bit regarding this point.

Lumps Hyla and Dryophytes as Hyla
Reasoning: SSAR hasn’t yet adopted this split, and it will be disruptive on iNaturalist

Indeed SSAR hasn't recognised Dryophytes yet, but the IUCN and AmphibiaWeb have (thank you @cliygh-and-mia for making the same comment 3 months ago), and as most Dryophytes are in North America, it doesn't bother people very much as the majority of iNat users are located there (or not in NE Asia at least). By working in North East Asia I'm in a very different position. Hyla crossed the Berring Bridge 60ish mya while Dryophytes did so about 16 mya. I don't have the exact divergence date in mind but I don't think it makes sense to anyone to pool Dryophytes and Hyla here, especially that there is literature supporting the split (Duellman 2016) and it has been recognised by other international leading groups.
On the other hand, there is one paper suggesting that Dryophytes suweonensis may be the same as D. immaculatus, based on a single individual, and the two species are pooled on iNat while it still is a debated question, the range of the two species is separated by the Yellow Sea and the calls are different (although unpublished).

I feel uncomfortable with the unbalanced reaction. Such a thing would not have happened for US or Eruoperan species, where indeed there may be more people active, as there is a clear lack of data.

So I agree and quote @cliygh-and-mia: "So, in principle, I agree with the idea to give priority to local external references for taxa that are locally endemic (but some problem will arise if two different local external references don't agree...)

I also like the recommendation from @jakob about adding a few columns to the Google doc where a bunch of things could be documented.

Regarding your question on a working group from iNat's top amphibian identifiers, I would be happy to help as much as I can.

Thank you for all the developments!

Amael

I can help some as well because I believe this could be a good thing and clear up a lot of the confusion. That being said have a few bones to pick with what has been clumped so far, mainly regarding US caudates. I must agree with @royaltyler on the dwarf split but I also believe that lumping of D. valentinei and D. auriculatus should not be done. This goes the same for the lumping of the E. spelaea complex. My reasoning behind this is because looking at the ASW it lists the papers published describing the species under the "comments" section. The reasoning is the same for the other species that I believe should stay lumped like the D. marmoratus complex. If you read the comments section on those species it will state that the species has yet to be formally described. I understand the inclusion of these species would call for more data and I believe I have the valentinei paper saved, or at least a range map. I know there was an E. spelaea complex map created I'll just need to search for that paper again. The use of amphibiaweb.org as a general reference is a good suggestion by @danieleseglie not just for Italian species. Overall though I think this is a great idea and like previously stated taxonomy in general is a hassle to deal with so I appreciate the effort.

Here's the 41 explicit discrepancies:

discrepancies = [
  {asw: ["Ichthophis cardamomensis"], inat: ["Ichthyophis cardamomensis"]},
  {asw: ["Ichthophis catlocensis"], inat: ["Ichthyophis catlocensis"]},
  {asw: ["Ichthophis chaloensis"], inat: ["Ichthyophis chaloensis"]},
  {asw: ["Microhyla mihintaleiWijayathilaka,"], inat: ["Microhyla mihintalei"]},
  {asw: ["Chlacorana crassiovis"], inat: ["Chalcorana crassiovis"]},
  {asw: [], inat: ["Dendropsophus nekronastes"]},
  {asw: [], inat: ["Hylodes caete"]},
  {asw: [], inat: ["Megophrys koui"]},  
  {asw: ["Aneides iecanus","Aneides niger","Aneides flavipunctatus"], inat: ["Aneides flavipunctatus"]},
  {asw: ["Desmognathus aureatus","Desmognathus melanius","Desmognathus marmoratus"], inat: ["Desmognathus marmoratus"]},
  {asw: ["Desmognathus auriculatus","Desmognathus valentinei"], inat: ["Desmognathus auriculatus"]},
  {asw: ["Pseudotriton diastictus","Pseudotriton montanus"], inat: ["Pseudotriton montanus"]},
  {asw: ["Trachycephalus typhonius","Trachycephalus macrotis","Trachycephalus quadrangulum","Trachycephalus vermiculatus"], inat: ["Trachycephalus typhonius"]},
  {asw: ["Dryophytes andersonii"], inat: ["Hyla andersonii"]},
  {asw: ["Dryophytes arboricola"], inat: ["Hyla arboricola"]},
  {asw: ["Dryophytes arenicolor"], inat: ["Hyla arenicolor"]} ,
  {asw: ["Dryophytes avivoca"], inat: ["Hyla avivoca"]},
  {asw: ["Dryophytes bocourti"], inat: ["Hyla bocourti"]},
  {asw: ["Dryophytes chrysoscelis"], inat: ["Hyla chrysoscelis"]},
  {asw: ["Dryophytes cinereus"], inat: ["Hyla cinerea"]},
  {asw: ["Dryophytes euphorbiaceus"], inat: ["Hyla euphorbiacea"]},
  {asw: ["Dryophytes eximius"], inat: ["Hyla eximia"]},
  {asw: ["Dryophytes femoralis"], inat: ["Hyla femoralis"]},
  {asw: ["Dryophytes gratiosus"], inat: ["Hyla gratiosa"]},
  {asw: ["Dryophytes immaculatus"], inat: ["Hyla immaculata"]},
  {asw: ["Dryophytes japonicus"], inat: ["Hyla japonica"]},
  {asw: ["Dryophytes plicatus"], inat: ["Hyla plicata"]},
  {asw: ["Dryophytes squirellus"], inat: ["Hyla squirella"]},
  {asw: ["Dryophytes versicolor"], inat: ["Hyla versicolor"]},
  {asw: ["Dryophytes walkeri"], inat: ["Hyla walkeri"]},
  {asw: ["Dryophytes wrightorum"], inat: ["Hyla wrightorum"]},
  {asw: ["Hyliola cadaverina"], inat: ["Pseudacris cadaverina"]},
  {asw: ["Hyliola hypochondriaca"], inat: ["Pseudacris hypochondriaca"]},
  {asw: ["Hyliola regilla"], inat: ["Pseudacris regilla"]},
  {asw: ["Hyliola sierra"], inat: ["Pseudacris sierra"]},
  {asw: ["Eurycea quadridigitata","Eurycea hillisi","Eurycea paludicola","Eurycea sphagnicola"], inat: ["Eurycea quadridigitata"]},
  {asw: ["Eurycea spelaea", "Eurycea nerea", "Eurycea braggi"], inat: ["Eurycea spelaea"]},  
  {asw: ["Bombina variegata"], inat: ["Bombina pachypus","Bombina variegata"]},
  {asw: ["Lissotriton graecus","Lissotriton vulgaris","Lissotriton meridionalis"], inat: ["Lissotriton vulgaris"]},
  {asw: ["Smilisca manisorum","Smilisca baudin"], inat: ["Smilisca baudin"]},
  {asw: ["Megophrus koui"], inat: ["Megophrys koui"]}
]

These discrepancies aside, iNaturalist should map to ASW. By this I mean if we run the above script to compare iNaturalist with ASW and there are any discrepancies not accounted for in our Explicit discrepancies, we should either update these discrepancies or update iNaturalist.
For example, imagine we no longer wanted to deviate from ASW via our “Aneides flavipunctatus merge” or “Bombina variegata split” coded in the discrepancies above. If we removed these and ran the script the output would read:

These are species in the iNat, not in ASW…
Bombina pachypus
These are species in ASW, not in the iNat…
Aneides iecanus
Aneides niger

Now lets consider addressing the species not in ASW. In this example they are Aneides iecanus and Aneides niger. Here the obvious action would be to create new taxa for Aneides iecanus and Aneides niger. But similar to the concept change caveat mentioned above, we must be wary that creating new taxa may unintentionally confuse the concepts of existing taxa. For example, Aneides flavipunctatus (sensu lato) includes salamanders not just from coastal California north of the San Francisco Bay (blue) but also salamanders from the Santa Cruz mountains south of San Francisco (pink) and salamanders inland around the Mount Shasta region (orange).

If we add Aneides niger as a species (salamanders Santa Cruz mountains south of San Francisco) this we are implying a change in the concept of Aneides flavipunctatus from senu lato to sensu stricto. Many bits of data associated with Aneides flavipunctatus (sensu lato) may no longer be suitable. For example, default taxon photos, taxon ranges, atlases, conservation statuses. Most importantly, observations of Aneides flavipunctatus from the Santa Cruz mountains must be re-identified as Aneides niger. For these reasons, it’s almost always easier and cleaner to split Aneides flavipunctatus (sensu lato) into Aneides iecanus and Aneides niger and a new Aneides flavipunctatus (sensu stricto) rather than trying to futz with Aneides flavipunctatus (sensu lato) to reinvent it as Aneides flavipunctatus (sensu stricto).

All these above mechanics of how to manage the amphibian taxonomy aside, we clearly need a way of deciding which explicit exceptions from ASW we need to make. More generally, there are actually a few decisions here that we need to make (or at least be aware that we’ve made them):

What taxonomic reference to use?
Currently, we’re curating from the Order Amphibia down to species. We aren’t actively curating subspecies, extinct taxa, or hybrids. We’re not including any non-standard nodes (e.g. subfamilies). Our external taxonomic reference is ASW with 41 explicit discrepancies mentioned above. Adding/removing additional explicit discrepancies need to be agreed upon.

How often do we update iNat to ASW?
I propose every three months proactively and reactively if someone complains (‘I observed species X which is in ASW why is it not in iNaturalist?’)

Who are the taxon curators and for how long?
The only people who can change the taxonomy of Amphibia on iNaturalist are now the Amphibia taxon curators. The role of the taxon curators is to help facilitate reaching consensus on any decisions affecting the taxonomy of Amphibians on iNaturalist (as I’m doing here) and also doing the tedious work of altering the taxonomy (as I just described above). We can have multiple taxon curators (ideally 1 to 2 more) and I’m proposing we serve for the duration of a year (starting now, but officially through 2018). Chime in if you want to be an ode taxon curator - but please do so if you have time to help me with the roles mentioned above.

Note on dispute resolution process...
In an ideal world, we all agree on these decisions. But I'd prefer we have a protocol in place for what to do if there's a disagreement that can't be resolved. My proposal is to set up an Amphibian taxonomic working group from top-identifiers similar to the one proposed for Odes here.

A working group consisting of the top 5 global amphib IDers + the top 3 IDers from each continent would result in a working group composed of the following people:
-=Global=-
herpguy, ritt, lucareptile, sandboa, danieleseglie
-=Europe=-
danieleseglie, leibele, jakob
-=Africa=-
jakob, alexanderr, mantellaman90
-=Oceania=-
adammyates,reiner,herpguy
-=North America=-
herpguy, ritt, lucareptile
-=Asia=-
amarzee,pintail,herpguy
-=South America=-
herpguy, diogoprov, iuvel

I've pasted a figure that shows these top-IDers in global context at the top of this post (and linked to here).

I propose that this working group is in effect for 2018. If there's any decision that needs to be made thats controversial, we post a link here to an online survey for voting with a deadline and this working group votes.

Does this sound like it could work?

Hi Scott! I completely agree with your proposal!
Concerning the working group composition, I agree with the "meritocracy based on community activity" selection, and also with that @jakob has just suggested (global top IDers + those from the regions).
Just some considerations on the additional taxonomic experts and how to most credibly select them...
Yes, having taxonomic experts might produce better outcomes but if they aren't very active on iNat (although they are already users) probably they don't have time to devote to the working group...
Could it be sufficient that working group members (at their own discretion) consult an external expert where necessary?
Otherwise, if it is opted to add "hand selected" taxonomic experts, I'd take the option 2 proposed by @loarie (First order of business by the working group is to appoint 2 additional members).
Best!
D.

@amarzee imho Russia, Mid East and Central Asia countries could be merged with Europe to make a sort of "extended" Western Palearctic zone, while China, Japan, Korea with South Asia to make a "restricted" (but still huge) Asia. Also North Africa could be put in the Palearctic "iNat zone".

The idea of selecting people from a bunch of major geographic regions came up to balance the bias of a largely North American user community and not so much to have these as specialists only assigned to the respective regions.

From @sandboa: "we need to add the two new species E. paludicola and E. sphagnicola to the this species group. They are both accepted by AMNH and SSAR."

In contrast to the journal post above, SSAR appears to now accept Eurycea hillisi, E. paludicola, and E. sphagnicola based on Wray 2017.

Edit to add: It's unclear to me whether taxon curators get notified when locked taxa are flagged, or what the correct protocol is in your hybrid curator/taxon curator system. Please let me know whether I should bother @ tagging you Scott and/or commenting on these journal posts (or Max for birds). Thanks!